I can confirm that the Gar-Class can have the deck gun mounted stern and bow (or should I say or?), whereas the Tambor-Class is "limited" to stern mounts.
So it is Class dependent. BUT ...
... Banjos method of only upgrading the thing you got, not only is the surefire way to go, it is not a disadvantage to have a stern mount. It's a saftey feature.
Stern mounts need a little more navigation, which you could translate to planning and a planned attack is a "safer" attack.
Also running and diving away at full speed from your target, might be safer then running and diving towards your target at full speed to dive under it into a curtain of depth charges.
I'll have to admit, that I kinda have gotten used to a stern mount. So please take my crazy rumblings as coming from someone who tries to make the best of what he has been given.